Hi Henrik,
I plot the density of 91:100 arrays, and found that the Array 91 is
too different from others. It's density value is much lower than
others.
I do not kown how to put the density picture here. I will send it to
your private email.
I think if I remove this array, then I will get the object. I will try
it later.
Thanks.
Hailei
On Oct 29, 5:42 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> Hi.
>
>
>
>
>
> On Wed, Oct 29, 2008 at 1:03 PM, hailei zhang <[EMAIL PROTECTED]> wrote:
> > Hi,
>
> > I have 228 paired snp arrays, the platform is snp250k_sty. I following the
> > steps which is provied on the aroma website.
> > When I runing the step of "Calibration for allelic crosstalk", I meet the
> > problem. After I run this commond "csAcc <-process(acc,verbose=log)",I can
> > not get the csAcc objec.
>
> > Thanks.
>
> > Hailei
>
> > When runing process function, I got this information:
> > List of 2
> > $ snps :List of 6
> > ..$ A/C: int [1:128036, 1:2] 2624 2678 2704 2706 2822 2840 3108 3180
> > 3262 3488 ...
> > .. ..- attr(*, "dimnames")=List of 2
> > .. .. ..$ : NULL
> > .. .. ..$ : chr [1:2] "A" "C"
> > ..$ A/G: int [1:557849, 1:2] 2588 2594 2604 2630 2636 2640 2642 2648
> > 2662 2682 ...
> > .. ..- attr(*, "dimnames")=List of 2
> > .. .. ..$ : NULL
> > .. .. ..$ : chr [1:2] "A" "G"
> > ..$ A/T: int [1:103336, 1:2] 2634 2654 2780 2800 2916 3054 3260 3388
> > 3586 3622 ...
> > .. ..- attr(*, "dimnames")=List of 2
> > .. .. ..$ : NULL
> > .. .. ..$ : chr [1:2] "A" "T"
> > ..$ C/G: int [1:156296, 1:2] 2572 2714 2730 2740 3006 3016 3030 3080
> > 3136 3170 ...
> > .. ..- attr(*, "dimnames")=List of 2
> > .. .. ..$ : NULL
> > .. .. ..$ : chr [1:2] "C" "G"
> > ..$ C/T: int [1:537767, 1:2] 2576 2578 2580 2646 2664 2672 2676 2680
> > 2708 2734 ...
> > .. ..- attr(*, "dimnames")=List of 2
> > .. .. ..$ : NULL
> > .. .. ..$ : chr [1:2] "C" "T"
> > ..$ G/T: int [1:118188, 1:2] 2602 2606 2656 2712 2854 2904 2966 2990
> > 3004 3040 ...
> > .. ..- attr(*, "dimnames")=List of 2
> > .. .. ..$ : NULL
> > .. .. ..$ : chr [1:2] "G" "T"
> > $ nonSNPs: NULL
> > - attr(*, "version")= int 1
> > 20081029 15:41:17| Reading all probe intensities...
> > 20081029 15:41:18| Reading all probe intensities...done
> > 20081029 15:41:18| Fitting calibration model...
> > 20081029 15:41:18| Allele probe-pair group #1 ('A/C') of 6...
> > 20081029 15:41:18| Fitting...
> > 20081029 15:41:18| Model/algorithm flavor: sfit
> > 20081029 15:41:18| Model parameters:
> > List of 3
> > $ alpha: num [1:5] 0.1 0.075 0.05 0.03 0.01
> > $ q : num 2
> > $ Q : num 98
> > 20081029 15:41:18| Number of data points: 128036
> > Error in solve.default(W) :
> > system is computationally singular: reciprocal condition number =
> > 3.02973e-25
> > 20081029 15:41:19| Fitting...done
> > 20081029 15:41:19| Allele probe-pair group #1 ('A/C') of 6...done
> > 20081029 15:41:19| Fitting calibration model...done
> > 20081029 15:41:19| Array #91
> > ('CHAMS_p_Sty31_(CO-124089)_Mapping250K_Sty_H09_112458') of 228...done
> > 20081029 15:41:19| Calibrating 228 arrays...done
> > 20081029 15:41:19|Calibrating data set for allelic cross talk...done
>
> Wow, I have run ACC (using the sfit algorithm) on tons of CEL files
> and I never observed a singularity problem this far. There is
> obviously something with Array #91 that causes the crosstalk estimator
> to fail. You could do some simple density plots to see if there is
> something funny going on with Array #91, e.g.
>
> # Extract Arrays 91-100
> cs2 <- extract(cs, 91:100);
> col <- rep("black", nbrOfArrays(cs2));
> col[1] <- "red";
> plotDensity(cs2, types="pm", col=col, lwd=2, ylim=c(0,0.5));
>
> Does Array #91 ("red") look the same as the others?
>
> What about if you do some spatial plots of the probe intensities?
> Seehttp://groups.google.com/group/aroma-affymetrix/web/exploratory-analy...
> for examples. If you use the ArrayExplorer you can specify which
> arrays you want to plot, e.g. process(ae, arrays=91:95). Does Array
> #91 look peculiar?
>
> If you can zip the
> CHAMS_p_Sty31_(CO-124089)_Mapping250K_Sty_H09_112458.CEL file and post
> it somewhere where I can download it, I can have a look at it. You can
> send me the download details offline to my private address if you want
> to.
>
> /Henrik
>
>
>
>
>
> > The following is my commonds:
>
> > library("aroma.affymetrix")
> > chipTypes <- c("Mapping250K_Sty")
> > cdfs <- AffymetrixCdfFile$byChipType(chipTypes)
> > dataSetName <- "snp_all"
> > csRawList <- list();
> > pairs <-
> > read.table(file="/home/hzhang/aroma/pairs_all.txt",sep="\t",header=T)
> > pairs <- as.matrix(pairs)
> > dim(pairs)
> > cs <- AffymetrixCelSet$byName(dataSetName, chipType=chipTypes);
> > stopifnot(all(getNames(cs) %in% pairs));
> > csRawList[[chipTypes]] <- cs;
> > gis <- getGenomeInformation(cdfs)
> > sis <- getSnpInformation(cdfs)
> > log <- Arguments$getVerbose(-4,timestamp=TRUE)
> > cs <- csRawList[[chipTypes]]
> > acc <- AllelicCrosstalkCalibration(cs)
> > csAcc <-process(acc,verbose=log)
> > ls()- Hide quoted text -
>
> - Show quoted text -- Hide quoted text -
>
> - Show quoted text -
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